ZRdb KZFP & Repeats
...

LTR_LTR86B1

  • Name
    LTR86B1
  • Repbase
    LTR86B1
  • Type
    LTR
  • Emergence
    99.0 Mya
  • Dfam Id
    DF0000608
Description :

5 bp TSDs, with a bias for NNNNC. Orientation based on ATTAAA siteconserved in other LTR86 consensuses.
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
tgcaggaatggacctcaggcaggcctgaagcctgggcctgctgagggatgctatgcctgggaaattgaccttcgnttcacccagtctcgcagtaaacactcaggaatgtgctggggttgttttgcaccagttacttgcacctggtgagcaggcaggcacgtagccagagtctccagaacagtcaggcggnagggagatgcagacaggagnntaaaactccccatgagaatggcaaagggagcttctcgcgcctggcggaatcctcactccgcgcgggtggtatcatccgcagctgtatgtccccatggggaactttgggggacctgggaagccgtacctccgtctgggagcatgctgcgttgtctcctgctttgtgtaaccgtctccgtaagtttccgtatcctttgccattaaagaaactttacatcctctaactgtgtctgttggcgtctttccgtcaatcacatcaccgtcccgttgtgacaaccacgca
Repeats structure For certain families, there exists a curated collection of TE-derived proteins, which constitutes a non-redundant set. As a results, several families may lack an associated coding sequences directly linked to them. The annotation for these families is obtained from Dfam. :
...
Peak overlapping A ChIP-seq peak of KZFPs that intersects with a certain repeats sequence on the genome. :
# KZFP name Record number KZFP age(Mya) Time correlation with Repeats
1 ZNF382 12 99.0 Highly correlated
2 ZNF100 4 28.9 Weakly correlated
3 ZNF558 4 99.0 Highly correlated
4 ZNF263 4 180.0 Weakly correlated
5 ZIM3 3 87.0 Moderately correlated
6 ZFP37 3 99.0 Highly correlated
7 ZNF766 3 43.0 Weakly correlated
8 ZNF394 2 99.0 Highly correlated
9 ZNF680 2 28.9 Weakly correlated
10 ZNF705B 2 28.9 Weakly correlated
11 ZNF789 2 99.0 Highly correlated
12 ZNF479 2 6.4 Weakly correlated
13 ZNF793 2 99.0 Highly correlated
14 ZNF317 2 99.0 Highly correlated
15 ZNF175 2 94.0 Moderately correlated
16 ZNF101 2 43.0 Weakly correlated
17 ZFP69B 2 99.0 Highly correlated
18 ZNF878 1 43.0 Weakly correlated
19 ZNF75D 1 94.0 Moderately correlated
20 ZNF723 1 15.2 Weakly correlated
21 ZNF705D 1 28.9 Weakly correlated
22 ZNF701 1 28.9 Weakly correlated
23 ZNF679 1 28.9 Weakly correlated
24 ZNF597 1 94.0 Moderately correlated
25 ZNF589 1 28.9 Weakly correlated
26 ZNF584 1 99.0 Highly correlated
27 ZNF554 1 99.0 Highly correlated
28 ZNF534 1 19.6 Weakly correlated
29 ZNF519 1 19.6 Weakly correlated
30 ZNF506 1 28.9 Weakly correlated
31 ZNF334 1 99.0 Highly correlated
32 ZNF257 1 0.0 Weakly correlated
KZFPs Motif in Repeats The motif of KZFPs found by the meme-chip appears in the repeats sequence. :
# KZFP name Record number KZFP age(Mya) Time correlation with Repeats
1 ZNF100 1 28.9 Weakly correlated
2 ZNF479 1 6.4 Weakly correlated
3 ZNF506 1 28.9 Weakly correlated
4 ZNF793 1 99.0 Highly correlated
5 ZNF878 1 43.0 Weakly correlated
6 ZNF789 1 99.0 Highly correlated
7 ZNF263 1 180.0 Weakly correlated
8 ZNF680 1 28.9 Weakly correlated
9 ZNF75D 1 94.0 Moderately correlated
KZFPs Motif in Repeats Consensus The motif of KZFPs found by the meme-chip can find the corresponding region on the consensus sequence of repeats. :
# KZFP name KZFP age(Mya) Time correlation with Repeats